Somatic variants lost when --genotype-germline-sites true
REQUIRED for all errors and issues:
a) GATK version used: 4.5.0.0
b) Exact command used:
I am calculating the exact same variants, in one case with default value for --genotype-germline-sites
Mutect2 -R /data/genome/hg38ucsc/hg38_no_alt.fa -I tumor.bam -I Tissue.bam -normal LH00280_109_22KKWNLT3_3_GAGTTACC --intervals intervals.bed.gz --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals 1000g_pon.hg38.vcf.gz --f1r2-tar-gz tumor.f1r2.tar.gz -O tumor_out.vcf.gz -bamout tumor_out.bam
And with --genotype-germline-sites true:
Mutect2 -R /data/genome/hg38ucsc/hg38_no_alt.fa -I tumor.bam -I Tissue.bam -normal LH00280_109_22KKWNLT3_3_GAGTTACC --intervals intervals.bed.gz --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals 1000g_pon.hg38.vcf.gz --genotype-germline-sites true --f1r2-tar-gz tumor.f1r2.tar.gz -O tumor_out.vcf.gz -bamout tumor_out.bam
My understanding is that by having all else equal and now doing --genotype-germline-sites true I should get all the other variants + some germline ones. In general this is the case but I get 12 variants (from , I checked them and most of them are justified with few counts, low quality of a significant fraction of the counts and/or less than 5% of allele frequency but there is one particular one which I can't figure out why it is in the somatic only version but not in the somatic + germline version:
chr11 1018406 . A T . . AS_SB_TABLE=68,91|2,4;DP=167;ECNT=4;MBQ=20,20;MFRL=203,194;MMQ=60,41;MPOS=20;NALOD=-3.700e+00;NLOD=10.16;POPAF=0.876;TLOD=3.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:77,3:0.046:80:26,1:14,1:61,2:35,42,1,2 0/1:82,3:0.045:85:30,1:10,0:62,2:33,49,1,2
The somatic version has the following counts for each base and relative frequency:
A G C T Total
90.06% 0.00% 0.00% 9.94% 100%
163 0 0 18 181
Seeing the bam signals in IGV (number of reads and quality: greyer is worse quality), I think in this case there is justification for a variant with T. Here is the somatic only bam IGV view:
This is the germline + somatic IGV view of the bam file:
What are the reasons why this particular variant is filtered in somatic + germline and not in somatic only?
Where are the "T" base reads in the somatic + germline bam file?
Is there something else I should be looking at to decide variants that I missed?
Is there an allele frequency cutoff where any allele less than X% is not considered despite evidence?
c) Entire program log:
Germline + somatic:
12:14:11.141 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:14:11.254 INFO Mutect2 - ------------------------------------------------------------
12:14:11.256 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
12:14:11.256 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
12:14:11.256 INFO Mutect2 - Executing as jaime@Nieves on Linux v5.15.0-116-generic amd64
12:14:11.256 INFO Mutect2 - Java runtime: Java HotSpot(TM) 64-Bit Server VM v22+36-2370
12:14:11.257 INFO Mutect2 - Start Date/Time: 18 de julio de 2024, 12:14:11 CEST
12:14:11.257 INFO Mutect2 - ------------------------------------------------------------
12:14:11.257 INFO Mutect2 - ------------------------------------------------------------
12:14:11.257 INFO Mutect2 - HTSJDK Version: 4.1.0
12:14:11.257 INFO Mutect2 - Picard Version: 3.1.1
12:14:11.257 INFO Mutect2 - Built for Spark Version: 3.5.0
12:14:11.257 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:14:11.258 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:14:11.258 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:14:11.258 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:14:11.258 INFO Mutect2 - Deflater: IntelDeflater
12:14:11.258 INFO Mutect2 - Inflater: IntelInflater
12:14:11.258 INFO Mutect2 - GCS max retries/reopens: 20
12:14:11.258 INFO Mutect2 - Requester pays: disabled
12:14:11.258 INFO Mutect2 - Initializing engine
12:14:11.344 INFO FeatureManager - Using codec VCFCodec to read file file:///data/somatic_variant_calling_resources/panel_of_normals_hg38/1000g_pon.hg38.vcf.gz
12:14:11.427 INFO FeatureManager - Using codec VCFCodec to read file file:///data/somatic_variant_calling_resources/af-only-gnomad.hg38.vcf.gz
12:14:11.500 INFO FeatureManager - Using codec BEDCodec to read file file:///data/Proc_La_Paz_Organoides_Muestras_Preliminares/variant_calling_somatic/Twist_Exome_RefSeq_targets_hg38.bed.gz
12:14:11.790 INFO IntervalArgumentCollection - Processing 36715240 bp from intervals
12:14:11.927 INFO Mutect2 - Done initializing engine
12:14:11.932 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
12:14:11.933 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
12:14:11.933 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
12:14:11.933 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
12:14:11.940 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
12:14:11.948 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
12:14:11.948 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
12:14:11.948 INFO IntelPairHmm - Available threads: 15
12:14:11.948 INFO IntelPairHmm - Requested threads: 15
12:14:11.948 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
12:14:12.000 INFO ProgressMeter - Starting traversal
12:14:12.000 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
12:14:22.084 INFO ProgressMeter - chr1:11228668 0.2 2080 12377.3
12:14:32.103 INFO ProgressMeter - chr1:20892619 0.3 3920 11699.7
12:14:42.117 INFO ProgressMeter - chr1:35269047 0.5 6350 12650.7
12:14:52.131 INFO ProgressMeter - chr1:47280241 0.7 8710 13022.4
12:15:02.150 INFO ProgressMeter - chr1:87104470 0.8 11400 13639.1
12:15:12.167 INFO ProgressMeter - chr1:114587387 1.0 13760 13721.8
12:15:22.199 INFO ProgressMeter - chr1:152213976 1.2 16340 13966.0
12:15:32.241 INFO ProgressMeter - chr1:158755716 1.3 18380 13743.6
12:15:42.260 INFO ProgressMeter - chr1:180945303 1.5 20720 13773.5
12:15:52.264 INFO ProgressMeter - chr1:206187279 1.7 23060 13799.6
12:16:02.291 INFO ProgressMeter - chr1:230249184 1.8 25400 13818.0
12:16:12.291 INFO ProgressMeter - chr2:9380741 2.0 27470 13701.8
12:16:22.309 INFO ProgressMeter - chr2:32782626 2.2 29910 13771.9
12:16:32.316 INFO ProgressMeter - chr2:72887548 2.3 32630 13952.8
12:16:42.341 INFO ProgressMeter - chr2:98192898 2.5 34960 13952.3
12:16:52.360 INFO ProgressMeter - chr2:132318309 2.7 37590 14064.6
12:17:02.367 INFO ProgressMeter - chr2:170859709 2.8 39950 14069.6
12:17:12.382 INFO ProgressMeter - chr2:197523624 3.0 42330 14080.2
12:17:22.385 INFO ProgressMeter - chr2:219448860 3.2 44630 14065.2
12:17:32.413 INFO ProgressMeter - chr2:240934916 3.3 46830 14020.0
12:17:42.429 INFO ProgressMeter - chr3:32734800 3.5 49210 14031.3
12:17:52.443 INFO ProgressMeter - chr3:48223503 3.7 51310 13965.5
12:18:02.447 INFO ProgressMeter - chr3:54782924 3.8 53580 13950.3
12:18:12.460 INFO ProgressMeter - chr3:108529263 4.0 55660 13888.4
12:18:22.465 INFO ProgressMeter - chr3:130593199 4.2 57940 13879.8
12:18:32.474 INFO ProgressMeter - chr3:170038076 4.3 60330 13897.0
12:18:43.282 INFO ProgressMeter - chr3:195782761 4.5 62210 13759.1
12:18:53.361 INFO ProgressMeter - chr4:2875916 4.7 63290 13496.5
12:19:03.395 INFO ProgressMeter - chr4:41646485 4.9 65510 13489.0
12:19:13.431 INFO ProgressMeter - chr4:81710014 5.0 67820 13499.7
12:19:23.476 INFO ProgressMeter - chr4:122243854 5.2 70150 13513.1
12:19:33.486 INFO ProgressMeter - chr4:176683926 5.4 72470 13525.3
12:19:43.503 INFO ProgressMeter - chr5:37003261 5.5 74740 13527.5
12:19:53.510 INFO ProgressMeter - chr5:79733715 5.7 77350 13589.6
12:20:03.554 INFO ProgressMeter - chr5:132899104 5.9 79880 13633.2
12:20:13.570 INFO ProgressMeter - chr5:147415709 6.0 81860 13584.1
12:20:23.589 INFO ProgressMeter - chr5:176877894 6.2 84030 13568.2
12:20:33.663 INFO ProgressMeter - chr6:26204945 6.4 86460 13592.1
12:20:43.728 INFO ProgressMeter - chr6:32093286 6.5 88140 13500.2
12:20:53.739 INFO ProgressMeter - chr6:41803806 6.7 89910 13428.1
12:21:03.746 INFO ProgressMeter - chr6:72182683 6.9 92120 13423.8
12:21:13.788 INFO ProgressMeter - chr6:112134467 7.0 94420 13431.4
12:21:23.796 INFO ProgressMeter - chr6:150823654 7.2 96700 13436.9
12:21:33.800 INFO ProgressMeter - chr7:5193118 7.4 98940 13436.8
12:21:43.848 INFO ProgressMeter - chr7:41706187 7.5 101300 13451.4
12:21:53.854 INFO ProgressMeter - chr7:80217303 7.7 103580 13456.2
12:22:03.882 INFO ProgressMeter - chr7:100890958 7.9 105740 13444.9
12:22:13.917 INFO ProgressMeter - chr7:105110771 8.0 106550 13265.8
12:22:23.917 INFO ProgressMeter - chr7:138752625 8.2 108750 13264.4
12:22:33.955 INFO ProgressMeter - chr7:151071689 8.4 110480 13206.0
12:22:43.977 INFO ProgressMeter - chr8:22513293 8.5 112660 13203.0
12:22:54.048 INFO ProgressMeter - chr8:58851524 8.7 115120 13231.0
12:23:04.051 INFO ProgressMeter - chr8:115620032 8.9 117740 13277.7
12:23:14.072 INFO ProgressMeter - chr8:144722544 9.0 120250 13310.0
12:23:24.116 INFO ProgressMeter - chr9:35074371 9.2 122300 13290.7
12:23:34.185 INFO ProgressMeter - chr9:87968095 9.4 124570 13294.9
12:23:44.224 INFO ProgressMeter - chr9:112875169 9.5 126690 13284.0
12:23:54.243 INFO ProgressMeter - chr9:128823747 9.7 128750 13267.7
12:24:04.269 INFO ProgressMeter - chr9:137142013 9.9 131020 13273.0
12:24:14.284 INFO ProgressMeter - chr10:31321526 10.0 133610 13310.3
12:24:24.327 INFO ProgressMeter - chr10:72274217 10.2 136160 13341.9
12:24:34.337 INFO ProgressMeter - chr10:98260922 10.4 138700 13372.2
12:24:44.346 INFO ProgressMeter - chr10:122461712 10.5 141210 13398.7
12:24:54.372 INFO ProgressMeter - chr11:1030213 10.7 142920 13349.3
12:25:04.374 INFO ProgressMeter - chr11:6921902 10.9 144430 13283.5
12:25:14.432 INFO ProgressMeter - chr11:43318447 11.0 146810 13297.4
12:25:24.466 INFO ProgressMeter - chr11:61282789 11.2 148830 13279.2
12:25:34.481 INFO ProgressMeter - chr11:66707816 11.4 151270 13298.8
12:25:44.526 INFO ProgressMeter - chr11:86672624 11.5 153600 13307.8
12:25:54.527 INFO ProgressMeter - chr11:118552214 11.7 156020 13325.0
12:26:04.548 INFO ProgressMeter - chr12:2859538 11.9 158220 13322.9
12:26:14.594 INFO ProgressMeter - chr12:20369885 12.0 160320 13312.0
12:26:24.629 INFO ProgressMeter - chr12:48777615 12.2 162470 13305.8
12:26:34.651 INFO ProgressMeter - chr12:56133417 12.4 164650 13302.3
12:26:44.664 INFO ProgressMeter - chr12:88125246 12.5 167210 13329.5
12:26:54.735 INFO ProgressMeter - chr12:113191734 12.7 169840 13360.3
12:27:04.742 INFO ProgressMeter - chr12:132816540 12.9 172230 13372.9
12:27:14.761 INFO ProgressMeter - chr13:51341092 13.0 174760 13395.7
12:27:24.773 INFO ProgressMeter - chr13:113667987 13.2 177060 13400.6
12:27:34.795 INFO ProgressMeter - chr14:31113104 13.4 179110 13386.5
12:27:44.802 INFO ProgressMeter - chr14:64939788 13.5 181530 13400.3
12:27:54.850 INFO ProgressMeter - chr14:93248476 13.7 183890 13408.8
12:28:05.643 INFO ProgressMeter - chr14:106359882 13.9 185790 13371.9
12:28:15.677 INFO ProgressMeter - chr15:40298798 14.1 187690 13348.0
12:28:25.721 INFO ProgressMeter - chr15:52244356 14.2 190130 13362.4
12:28:35.747 INFO ProgressMeter - chr15:74197338 14.4 192540 13374.8
12:28:45.774 INFO ProgressMeter - chr15:90946614 14.6 194780 13375.1
12:28:55.810 INFO ProgressMeter - chr16:3356541 14.7 197230 13389.5
12:29:05.830 INFO ProgressMeter - chr16:21726523 14.9 199510 13392.5
12:29:15.839 INFO ProgressMeter - chr16:46957029 15.1 201870 13400.8
12:29:25.860 INFO ProgressMeter - chr16:68254919 15.2 204130 13402.3
12:29:35.969 INFO ProgressMeter - chr16:88436013 15.4 206330 13398.5
12:29:45.997 INFO ProgressMeter - chr17:5539415 15.6 208570 13398.5
12:29:56.028 INFO ProgressMeter - chr17:16431966 15.7 210670 13389.6
12:30:06.057 INFO ProgressMeter - chr17:35844477 15.9 213160 13405.5
12:30:16.076 INFO ProgressMeter - chr17:43545574 16.1 215600 13418.0
12:30:26.080 INFO ProgressMeter - chr17:58755998 16.2 218020 13429.3
12:30:36.100 INFO ProgressMeter - chr17:75843014 16.4 220540 13446.2
12:30:46.113 INFO ProgressMeter - chr18:6975937 16.6 223040 13461.6
12:30:56.117 INFO ProgressMeter - chr18:51078256 16.7 225470 13472.7
12:31:06.131 INFO ProgressMeter - chr19:2934089 16.9 227980 13488.2
12:31:16.188 INFO ProgressMeter - chr19:8957319 17.1 230240 13488.1
12:31:26.199 INFO ProgressMeter - chr19:15424700 17.2 232610 13495.1
12:31:36.208 INFO ProgressMeter - chr19:32826683 17.4 234870 13495.6
12:31:46.263 INFO ProgressMeter - chr19:40465671 17.6 237240 13501.8
12:31:56.297 INFO ProgressMeter - chr19:47417178 17.7 239470 13500.2
12:32:06.329 INFO ProgressMeter - chr19:53266760 17.9 241750 13501.5
12:32:16.334 INFO ProgressMeter - chr19:58572550 18.1 243650 13482.0
12:32:26.354 INFO ProgressMeter - chr20:33002861 18.2 246080 13491.8
12:32:36.366 INFO ProgressMeter - chr20:49849579 18.4 248500 13501.0
12:32:46.389 INFO ProgressMeter - chr21:32350704 18.6 250950 13511.4
12:32:56.399 INFO ProgressMeter - chr22:19479083 18.7 253440 13524.0
12:33:06.422 INFO ProgressMeter - chr22:32152067 18.9 255800 13529.4
12:33:16.462 INFO ProgressMeter - chr22:49885163 19.1 258240 13538.6
12:33:26.502 INFO ProgressMeter - chrX:24310862 19.2 260310 13528.4
12:33:36.531 INFO ProgressMeter - chrX:52948247 19.4 262250 13511.9
12:33:46.654 INFO ProgressMeter - chrX:85268294 19.6 264120 13491.0
12:33:56.654 INFO ProgressMeter - chrX:124081380 19.7 266060 13475.3
12:34:06.682 INFO ProgressMeter - chrX:154359484 19.9 267960 13457.6
12:34:08.476 INFO Mutect2 - 2383762 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
14925 read(s) filtered by: NotSecondaryAlignmentReadFilter
5998852 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
69 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
8397608 total reads filtered out of 71363338 reads processed
12:34:08.476 INFO ProgressMeter - chrY:57196636 19.9 269070 13493.1
12:34:08.476 INFO ProgressMeter - Traversal complete. Processed 269070 total regions in 19.9 minutes.
12:34:08.808 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.400759688
12:34:08.808 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 34.628770165
12:34:08.808 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 5.79 sec
12:34:10.996 INFO Mutect2 - Shutting down engine
[18 de julio de 2024, 12:34:10 CEST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 20.00 minutes.
Runtime.totalMemory()=704643072
Using GATK jar /opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar
Running:
#Same command as before
Somatic only:
11:54:40.721 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:54:40.886 INFO Mutect2 - ------------------------------------------------------------
11:54:40.889 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
11:54:40.889 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
11:54:40.889 INFO Mutect2 - Executing as jaime@Nieves on Linux v5.15.0-116-generic amd64
11:54:40.889 INFO Mutect2 - Java runtime: Java HotSpot(TM) 64-Bit Server VM v22+36-2370
11:54:40.889 INFO Mutect2 - Start Date/Time: 18 de julio de 2024, 11:54:40 CEST
11:54:40.889 INFO Mutect2 - ------------------------------------------------------------
11:54:40.889 INFO Mutect2 - ------------------------------------------------------------
11:54:40.890 INFO Mutect2 - HTSJDK Version: 4.1.0
11:54:40.890 INFO Mutect2 - Picard Version: 3.1.1
11:54:40.890 INFO Mutect2 - Built for Spark Version: 3.5.0
11:54:40.890 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:54:40.890 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:54:40.891 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:54:40.891 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:54:40.891 INFO Mutect2 - Deflater: IntelDeflater
11:54:40.891 INFO Mutect2 - Inflater: IntelInflater
11:54:40.891 INFO Mutect2 - GCS max retries/reopens: 20
11:54:40.891 INFO Mutect2 - Requester pays: disabled
11:54:40.891 INFO Mutect2 - Initializing engine
11:54:40.991 INFO FeatureManager - Using codec VCFCodec to read file file:///data/somatic_variant_calling_resources/panel_of_normals_hg38/1000g_pon.hg38.vcf.gz
11:54:41.063 INFO FeatureManager - Using codec VCFCodec to read file file:///data/somatic_variant_calling_resources/af-only-gnomad.hg38.vcf.gz
11:54:41.124 INFO FeatureManager - Using codec BEDCodec to read file file:///data/Proc_La_Paz_Organoides_Muestras_Preliminares/variant_calling_somatic/Twist_Exome_RefSeq_targets_hg38.bed.gz
11:54:41.375 INFO IntervalArgumentCollection - Processing 36715240 bp from intervals
11:54:41.510 INFO Mutect2 - Done initializing engine
11:54:41.516 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
11:54:41.517 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
11:54:41.518 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
11:54:41.518 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
11:54:41.527 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
11:54:41.536 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
11:54:41.536 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
11:54:41.537 INFO IntelPairHmm - Available threads: 15
11:54:41.537 INFO IntelPairHmm - Requested threads: 15
11:54:41.537 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
11:54:41.588 INFO ProgressMeter - Starting traversal
11:54:41.588 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
11:54:51.602 INFO ProgressMeter - chr1:11833877 0.2 2220 13302.7
11:55:01.626 INFO ProgressMeter - chr1:23193086 0.3 4270 12786.3
11:55:11.641 INFO ProgressMeter - chr1:38023545 0.5 6830 13636.4
11:55:21.651 INFO ProgressMeter - chr1:54679263 0.7 9410 14093.2
11:55:31.666 INFO ProgressMeter - chr1:99900636 0.8 12160 14569.6
11:55:41.694 INFO ProgressMeter - chr1:145978361 1.0 14810 14784.4
11:55:51.695 INFO ProgressMeter - chr1:155048994 1.2 17050 14592.2
11:56:01.715 INFO ProgressMeter - chr1:169380481 1.3 19460 14572.0
11:56:11.807 INFO ProgressMeter - chr1:201213199 1.5 21930 14584.8
11:56:21.842 INFO ProgressMeter - chr1:225207033 1.7 24460 14639.0
11:56:31.898 INFO ProgressMeter - chr1:248441845 1.8 26790 14571.8
11:56:41.919 INFO ProgressMeter - chr2:28998143 2.0 29280 14599.9
11:56:51.959 INFO ProgressMeter - chr2:70181709 2.2 32090 14768.7
11:57:01.969 INFO ProgressMeter - chr2:97551289 2.3 34590 14784.2
11:57:12.021 INFO ProgressMeter - chr2:134991537 2.5 37420 14925.0
11:57:22.028 INFO ProgressMeter - chr2:175136412 2.7 40030 14970.2
11:57:32.029 INFO ProgressMeter - chr2:202113336 2.8 42500 14961.3
11:57:42.051 INFO ProgressMeter - chr2:229227957 3.0 44970 14951.6
11:57:52.076 INFO ProgressMeter - chr3:10073253 3.2 47490 14958.6
11:58:02.118 INFO ProgressMeter - chr3:42686756 3.3 49940 14942.5
11:58:12.171 INFO ProgressMeter - chr3:51863287 3.5 52350 14915.8
11:58:22.194 INFO ProgressMeter - chr3:98149386 3.7 54660 14866.4
11:58:32.228 INFO ProgressMeter - chr3:129003309 3.8 57190 14877.8
11:58:42.246 INFO ProgressMeter - chr3:168010743 4.0 59760 14899.2
11:58:52.661 INFO ProgressMeter - chr3:195782921 4.2 61740 14754.3
11:59:02.669 INFO ProgressMeter - chr4:4417235 4.4 63080 14496.7
11:59:12.698 INFO ProgressMeter - chr4:49017249 4.5 65460 14487.2
11:59:22.709 INFO ProgressMeter - chr4:88431162 4.7 67900 14492.0
11:59:32.718 INFO ProgressMeter - chr4:144718875 4.9 70390 14507.0
11:59:42.732 INFO ProgressMeter - chr5:1480942 5.0 72870 14518.7
11:59:52.758 INFO ProgressMeter - chr5:62306473 5.2 75370 14532.9
12:00:02.766 INFO ProgressMeter - chr5:113001084 5.4 78140 14597.6
12:00:12.816 INFO ProgressMeter - chr5:141194353 5.5 80540 14589.4
12:00:22.821 INFO ProgressMeter - chr5:168441682 5.7 82680 14537.9
12:00:32.854 INFO ProgressMeter - chr6:15593059 5.9 85200 14553.1
12:00:42.904 INFO ProgressMeter - chr6:31815757 6.0 87110 14465.5
12:00:52.947 INFO ProgressMeter - chr6:42106863 6.2 89270 14423.3
12:01:02.962 INFO ProgressMeter - chr6:75898373 6.4 91740 14433.1
12:01:12.970 INFO ProgressMeter - chr6:125752007 6.5 94280 14453.4
12:01:22.996 INFO ProgressMeter - chr6:159688126 6.7 96700 14454.2
12:01:33.018 INFO ProgressMeter - chr7:23155991 6.9 99330 14485.6
12:01:43.049 INFO ProgressMeter - chr7:72807066 7.0 101900 14506.7
12:01:53.102 INFO ProgressMeter - chr7:100175760 7.2 104490 14528.9
12:02:03.125 INFO ProgressMeter - chr7:104126848 7.4 105670 14359.4
12:02:13.157 INFO ProgressMeter - chr7:139961919 7.5 108090 14362.0
12:02:23.202 INFO ProgressMeter - chr7:156966270 7.7 110140 14315.9
12:02:33.231 INFO ProgressMeter - chr8:28329158 7.9 112460 14306.6
12:02:43.241 INFO ProgressMeter - chr8:74825460 8.0 114990 14324.5
12:02:53.257 INFO ProgressMeter - chr8:132095703 8.2 117590 14349.9
12:03:03.281 INFO ProgressMeter - chr9:8521426 8.4 120030 14355.0
12:03:13.334 INFO ProgressMeter - chr9:38423965 8.5 122010 14305.2
12:03:23.344 INFO ProgressMeter - chr9:96958835 8.7 124390 14304.4
12:03:33.368 INFO ProgressMeter - chr9:122226376 8.9 126500 14272.8
12:03:43.424 INFO ProgressMeter - chr9:132678461 9.0 128590 14239.4
12:03:53.445 INFO ProgressMeter - chr10:7727703 9.2 130960 14238.5
12:04:03.446 INFO ProgressMeter - chr10:49165766 9.4 133570 14263.8
12:04:13.469 INFO ProgressMeter - chr10:84222220 9.5 135960 14264.5
12:04:23.503 INFO ProgressMeter - chr10:102656747 9.7 138430 14273.2
12:04:33.510 INFO ProgressMeter - chr10:131970864 9.9 140760 14268.1
12:04:43.513 INFO ProgressMeter - chr11:1889445 10.0 142210 14175.5
12:04:53.516 INFO ProgressMeter - chr11:17155526 10.2 144250 14143.8
12:05:03.562 INFO ProgressMeter - chr11:48142919 10.4 146520 14134.4
12:05:13.605 INFO ProgressMeter - chr11:63765923 10.5 148470 14094.9
12:05:23.631 INFO ProgressMeter - chr11:71484312 10.7 150890 14100.9
12:05:33.665 INFO ProgressMeter - chr11:101961741 10.9 153120 14089.2
12:05:43.671 INFO ProgressMeter - chr11:123606609 11.0 155490 14091.0
12:05:53.715 INFO ProgressMeter - chr12:6912730 11.2 157610 14069.7
12:06:03.715 INFO ProgressMeter - chr12:31103317 11.4 159840 14059.6
12:06:13.719 INFO ProgressMeter - chr12:51206789 11.5 161910 14035.8
12:06:23.724 INFO ProgressMeter - chr12:57613440 11.7 164120 14024.7
12:06:33.736 INFO ProgressMeter - chr12:101299973 11.9 166700 14044.9
12:06:43.768 INFO ProgressMeter - chr12:120641216 12.0 169150 14053.3
12:06:53.841 INFO ProgressMeter - chr13:25097959 12.2 171480 14050.9
12:07:03.843 INFO ProgressMeter - chr13:75841928 12.4 173910 14058.0
12:07:13.852 INFO ProgressMeter - chr14:21076563 12.5 176130 14048.0
12:07:23.876 INFO ProgressMeter - chr14:46651092 12.7 178390 14041.2
12:07:33.893 INFO ProgressMeter - chr14:73265370 12.9 180780 14044.7
12:07:43.915 INFO ProgressMeter - chr14:101894507 13.0 183120 14044.3
12:07:54.198 INFO ProgressMeter - chr15:23443777 13.2 184640 13977.1
12:08:04.236 INFO ProgressMeter - chr15:42734226 13.4 187100 13986.2
12:08:14.254 INFO ProgressMeter - chr15:64171931 13.5 189620 13999.9
12:08:24.273 INFO ProgressMeter - chr15:81332719 13.7 191990 14002.2
12:08:34.299 INFO ProgressMeter - chr16:734229 13.9 194210 13993.6
12:08:44.340 INFO ProgressMeter - chr16:14552021 14.0 196710 14004.9
12:08:54.360 INFO ProgressMeter - chr16:30225514 14.2 199250 14019.0
12:09:04.364 INFO ProgressMeter - chr16:66392136 14.4 201550 14016.4
12:09:14.367 INFO ProgressMeter - chr16:81108630 14.5 203860 14014.6
12:09:24.378 INFO ProgressMeter - chr17:4086486 14.7 206210 14015.4
12:09:34.402 INFO ProgressMeter - chr17:10497069 14.9 208350 14001.8
12:09:44.403 INFO ProgressMeter - chr17:30316687 15.0 210650 13999.6
12:09:54.404 INFO ProgressMeter - chr17:41624078 15.2 213010 14001.3
12:10:04.415 INFO ProgressMeter - chr17:50191788 15.4 215310 13999.0
12:10:14.424 INFO ProgressMeter - chr17:69029169 15.5 217630 13998.0
12:10:24.449 INFO ProgressMeter - chr17:80893799 15.7 219840 13989.8
12:10:34.452 INFO ProgressMeter - chr18:25224345 15.9 222250 13994.7
12:10:44.477 INFO ProgressMeter - chr18:74634920 16.0 224500 13989.2
12:10:54.540 INFO ProgressMeter - chr19:4910847 16.2 226800 13986.3
12:11:04.547 INFO ProgressMeter - chr19:10357464 16.4 228780 13964.8
12:11:14.569 INFO ProgressMeter - chr19:16654035 16.5 230950 13955.0
12:11:24.598 INFO ProgressMeter - chr19:34221807 16.7 233040 13940.5
12:11:34.620 INFO ProgressMeter - chr19:40397509 16.9 235200 13930.5
12:11:44.657 INFO ProgressMeter - chr19:46658765 17.1 237200 13911.1
12:11:54.673 INFO ProgressMeter - chr19:52066007 17.2 239370 13902.3
12:12:04.702 INFO ProgressMeter - chr19:57500081 17.4 241100 13868.1
12:12:14.744 INFO ProgressMeter - chr20:21706524 17.6 243330 13862.9
12:12:24.766 INFO ProgressMeter - chr20:44511289 17.7 245520 13855.8
12:12:34.778 INFO ProgressMeter - chr20:63547108 17.9 247680 13847.3
12:12:44.798 INFO ProgressMeter - chr21:43053880 18.1 249950 13845.0
12:12:54.827 INFO ProgressMeter - chr22:23870008 18.2 252200 13841.5
12:13:04.922 INFO ProgressMeter - chr22:37953788 18.4 254290 13828.5
12:13:14.951 INFO ProgressMeter - chr22:50715669 18.6 256560 13826.2
12:13:24.952 INFO ProgressMeter - chrX:30700414 18.7 258260 13793.9
12:13:35.017 INFO ProgressMeter - chrX:53210414 18.9 260040 13765.7
12:13:45.082 INFO ProgressMeter - chrX:83871452 19.1 261780 13735.8
12:13:55.104 INFO ProgressMeter - chrX:119758668 19.2 263480 13704.9
12:14:05.147 INFO ProgressMeter - chrX:153565818 19.4 265300 13680.5
12:14:09.092 INFO Mutect2 - 2383762 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
14925 read(s) filtered by: NotSecondaryAlignmentReadFilter
5998852 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
69 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
8397608 total reads filtered out of 71363338 reads processed
12:14:09.092 INFO ProgressMeter - chrY:57196636 19.5 266790 13710.8
12:14:09.092 INFO ProgressMeter - Traversal complete. Processed 266790 total regions in 19.5 minutes.
12:14:09.384 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.351840672
12:14:09.384 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 30.332537157
12:14:09.384 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 5.31 sec
12:14:10.044 INFO Mutect2 - Shutting down engine
[18 de julio de 2024, 12:14:10 CEST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 19.49 minutes.
Runtime.totalMemory()=1174405120
Using GATK jar /opt/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar
Running:
#Same command as before
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My first pick is on that interval parameter which definitely affects the way local assembly and realignment.
Can you try adding more padding to those intervals by using parameter -ip ?
We recommend adding preferably around 150 to 250 basepair padding for all intervals. In fact you might also try running it without the interval parameter to see if you observe the same issue. Intervals limit the amount of reference genome and read content involved in generating the local assembly therefore detected variants may still be affected undeterministically (albeit a small fraction).
I hope this helps.
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Is the issue that the variant is emitted but filtered with --genotype-germline-sites, but it is PASS otherwise? I don't know the filter applied in your case, but I noted some months ago that if you emit more variants (e.g. by --genotype-germline-sites), the clustered_mutations filter starts going to work and filtering out some high quality somatic variants. If this is your issue, I believe the fix was implemented in 4.6.0.0, released in June.
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This particular PR is the one you are talking about I suppose. This could be the solution as well. Thanks for pointing out.
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3 comments